Bioc-devel - September 2017 - Date View

Friday, September 29, 2017 14 emails

Hervé Pagès Final List of Deprecated Packages for Bioc3.6 Hervé Pagès Something about time out errors Obenchain, Valerie Mac Workflow builds Martin Morgan Problem building package with devtools+Rcpp Shepherd, Lori Final List of Deprecated Packages for Bioc3.6 Shepherd, Lori Something about time out errors Tim Triche, Jr. "chartr" method for MaskedXString objects with active masks not ready yet Please complain! Eric Frichot Failing package LEA Turaga, Nitesh Failing package LEA Turaga, Nitesh Failing package LEA Turaga, Nitesh Several ssh keys ? Sean Davis Moving from development build to release build Samuel Wieczorek Several ssh keys ? Aaron Lun strange error in Jenkins build forsingleCellWorkflow

Thursday, September 28, 2017 8 emails

Yong Kee Tan Moving from development build to release build Jialin Ma Printing DataFrame with nested data.frame/DataFrame/DataFrameList Hervé Pagès Printing DataFrame with nested data.frame/DataFrame/DataFrameList Hervé Pagès writing unit tests for functions in an initializer Michael Lawrence writing unit tests for functions in an initializer Kasper Daniel Hansen writing unit tests for functions in an initializer Zach Skidmore writing unit tests for functions in an initializer Jialin Ma Printing DataFrame with nested data.frame/DataFrame/DataFrameList

Wednesday, September 27, 2017 11 emails

Hervé Pagès R: R: R: Errors updating DaMiRseq package Andrzej Oleś R: R: R: Errors updating DaMiRseq package Hervé Pagès R: R: R: Errors updating DaMiRseq package Hervé Pagès R: R: R: Errors updating DaMiRseq package Aimin Yan Something about time out errors Turaga, Nitesh Need write permission for CNPBayes Robert Scharpf Need write permission for CNPBayes Leo Lahti New package for microbiome (mostly 16S) data analysis jmason Cannot clone PhenStat sergi.picart at upc.edu Problem building package with devtools+Rcpp Sergi P Problem building package with devtools+Rcpp

Tuesday, September 26, 2017 7 emails

Vincent Carey strange error in Jenkins build forsingleCellWorkflow Vincent Carey strange error in Jenkins build forsingleCellWorkflow Mattia Chiesa R: R: R: Errors updating DaMiRseq package Shian Su strange error in Jenkins build forsingleCellWorkflow Martin Morgan biocLite and automatic installing of packages Imports packages Martin Morgan strange error in Jenkins build forsingleCellWorkflow Aaron Lun strange error in Jenkins build forsingleCellWorkflow

Monday, September 25, 2017 10 emails

Stefan Mutter biocLite and automatic installing of packages Imports packages Turaga, Nitesh Need write permission for CNPBayes Robert Scharpf Need write permission for CNPBayes Turaga, Nitesh failing Biocondcutor package funtooNorm Turaga, Nitesh failing Biocondcutor package funtooNorm Matt Richards Change push privileges on MotifDb Lluís Revilla Support site question can't be edited: Language "ca" is not one of the supported languages ['en']! Turaga, Nitesh SSH keys Turaga, Nitesh Cannot clone PhenStat jmason Cannot clone PhenStat

Saturday, September 23, 2017 7 emails

Mattia Chiesa R: R: Errors updating DaMiRseq package Martin Morgan Change push privileges on MotifDb Martin Morgan Need write permission for CNPBayes Martin Morgan R: Errors updating DaMiRseq package Mattia Chiesa R: Errors updating DaMiRseq package Robert Scharpf Need write permission for CNPBayes jmason Cannot clone PhenStat

Friday, September 22, 2017 9 emails

Aaron Lun assay dimnames in SingleCellExperiment / SummarizedExperiment Hervé Pagès assay dimnames in SingleCellExperiment / SummarizedExperiment Hervé Pagès Question about inclusion in upcoming bioconductor Matt Richards Change push privileges on MotifDb Turaga, Nitesh Errors updating DaMiRseq package Mattia Chiesa Errors updating DaMiRseq package Turaga, Nitesh Bad keys Martin Morgan Vignette figures are wrong size Christopher John Vignette figures are wrong size

Thursday, September 21, 2017 10 emails

Martin Morgan Cannot clone PhenStat jmason Cannot clone PhenStat Siddhartha Bagaria Announcing Bazel for R packages Turaga, Nitesh Unable to push to https://git.bioconductor.org/packages/GenomicTuples Peter Hickey Unable to push to https://git.bioconductor.org/packages/GenomicTuples Turaga, Nitesh Unable to push to https://git.bioconductor.org/packages/GenomicTuples Peter Hickey Unable to push to https://git.bioconductor.org/packages/GenomicTuples Turaga, Nitesh maintain immunoClust Sörensen, Till Antoni maintain immunoClust Shepherd, Lori Deadline for Packages and Data Bioc3.6

Wednesday, September 20, 2017 7 emails

Hervé Pagès Generic for write to BiocGenerics Hervé Pagès strange error in Jenkins build forsingleCellWorkflow Laurent Gatto Generic for write to BiocGenerics Hervé Pagès Generic for write to BiocGenerics Shepherd, Lori Workflows now building with Bioc3.6 Obenchain, Valerie Bioconductor 3.6 release Martin Morgan Support site question can't be edited: Language "ca" is not one of the supported languages ['en']!

Tuesday, September 19, 2017 11 emails

Gordon K Smyth Support site question can't be edited: Language "ca" is not one of the supported languages ['en']! Aaron Lun strange error in Jenkins build forsingleCellWorkflow Wolfgang Huber strange error in Jenkins build forsingleCellWorkflow Rodriguez Martinez, Andrea VIGNETTES IN DEVEL Martin Morgan strange error in Jenkins build forsingleCellWorkflow jmason Cannot clone PhenStat Wolfgang Huber strange error in Jenkins build forsingleCellWorkflow Shepherd, Lori VIGNETTES IN DEVEL Martin Morgan strange error in Jenkins build forsingleCellWorkflow Rodriguez Martinez, Andrea VIGNETTES IN DEVEL Aaron Lun strange error in Jenkins build forsingleCellWorkflow

Monday, September 18, 2017 12 emails

Laurent Gatto Generic for write to BiocGenerics Rainer Johannes Generic for write to BiocGenerics Shian Su strange error in Jenkins build forsingleCellWorkflow Aaron Lun strange error in Jenkins build forsingleCellWorkflow Michael Lawrence Generic for write to BiocGenerics Hervé Pagès Generic for write to BiocGenerics Turaga, Nitesh hook declined to update error Turaga, Nitesh hook declined error Rainer Johannes Generic for write to BiocGenerics Lluís Revilla BioCor devel timeout Anand MT hook declined to update error Anand MT hook declined error

Sunday, September 17, 2017 2 emails

Paul Murrell ggplot error Error in grid.Call.graphics Shepherd, Lori Question about inclusion in upcoming bioconductor

Saturday, September 16, 2017 4 emails

Vincent Carey strange error in Jenkins build forsingleCellWorkflow Aaron Lun strange error in Jenkins build forsingleCellWorkflow Kevin RUE assay dimnames in SingleCellExperiment / SummarizedExperiment Martin Morgan strange error in Jenkins build forsingleCellWorkflow

Friday, September 15, 2017 14 emails

Aaron Lun strange error in Jenkins build forsingleCellWorkflow Aaron Lun assay dimnames in SingleCellExperiment / SummarizedExperiment Ioannis Vardaxis Problems with vignette and makeovers file Samuel E Zimmerman ggplot error Error in grid.Call.graphics Weirather, Jason L. Question about inclusion in upcoming bioconductor Martin Morgan TLS error in vignette on all devel builds Carlos Ruiz Bioconductor failing package MEAL Nan Xiao TLS error in vignette on all devel builds Turaga, Nitesh Unable to create a remote branch Andrzej Oleś BiocStyle not acknowledging fig.wide=TRUE in knitr Vladimir Kiselev TLS error in vignette on all devel builds Samuel Wieczorek Unable to create a remote branch Samuel Wieczorek Unable to create a remote branch Aaron Lun BiocStyle not acknowledging fig.wide=TRUE in knitr

Thursday, September 14, 2017 20 emails

Michael Love workflow builder error: winbuilder1 says "pdflatex is not available" Hervé Pagès Identical methods in two packages Andrzej Oleś workflow builder error: winbuilder1 says "pdflatex is not available" Laurent Gatto Identical methods in two packages Turaga, Nitesh Bioconductor failing package MEAL Turaga, Nitesh Bioconductor failing package MEAL Turaga, Nitesh Bioconductor failing package MEAL Carlos Ruiz Bioconductor failing package MEAL Tomasz Stokowy Hsapiens in bioconductor Turaga, Nitesh Getting w+r access for my package (IntEREst); svn/git transfer problem (Problem remains unsloved) Turaga, Nitesh Bioconductor failing package MEAL Michael Love workflow builder error: winbuilder1 says "pdflatex is not available" Hervé Pagès Identical methods in two packages Hervé Pagès Hsapiens in bioconductor Vincent Carey Hsapiens in bioconductor Turaga, Nitesh SSH keys Piotr Balwierz Hsapiens in bioconductor Vincent Carey non-ASCII strings in data for a developing package Tomasz Stokowy Hsapiens in bioconductor Kevin RUE assay dimnames in SingleCellExperiment / SummarizedExperiment

Wednesday, September 13, 2017 11 emails

Hervé Pagès coerce ExpressionSet to SummarizedExperiment Hervé Pagès coerce ExpressionSet to SummarizedExperiment Ludwig Geistlinger coerce ExpressionSet to SummarizedExperiment Marcel Ramos MultiAssayExperiment Subsetting Fails if Column Data Has One Column Marcel Ramos ExperimentList Contructor Failing Ludwig Geistlinger BiocStyle2: issue with wide figure command Karim Mezhoud Creating an org.Hs.uniprot.db package Aditya Bhagwat Creating an org.Hs.uniprot.db package Karim Mezhoud Creating an org.Hs.uniprot.db package Vincent Carey Creating an org.Hs.uniprot.db package Markus List failing Bioconductor package DeepBlueR

Tuesday, September 12, 2017 33 emails

Aditya Bhagwat Creating an org.Hs.uniprot.db package Rainer Johannes Creating an org.Hs.uniprot.db package Dario Strbenac MultiAssayExperiment Subsetting Fails if Column Data Has One Column Dario Strbenac ExperimentList Contructor Failing Hervé Pagès Identical methods in two packages Andrzej Oleś BiocStyle2: issue with wide figure command Ludwig Geistlinger BiocStyle2: issue with wide figure command Vincent Carey Identical methods in two packages Michael Lawrence Identical methods in two packages Laurent Gatto Identical methods in two packages Turaga, Nitesh problem with git / svn transition: ssh keys Luo Weijun problem with git / svn transition: ssh keys Turaga, Nitesh problem with git / svn transition: ssh keys Luo Weijun problem with git / svn transition: ssh keys Hervé Pagès Identical methods in two packages Turaga, Nitesh problem with git / svn transition: ssh keys Marcel Ramos ExperimentList Contructor Failing Luo Weijun problem with git / svn transition: ssh keys Hervé Pagès failing Bioconductor package DeepBlueR Turaga, Nitesh problem with git / svn transition: ssh keys Hervé Pagès clarifying initialization for BiocCheck Ludwig Geistlinger clarifying initialization for BiocCheck Turaga, Nitesh updating Bioconductor package that is already on Github Turaga, Nitesh Hook declined on a branch Robert Castelo GenomicRanges::cbind() problem Markus List failing Bioconductor package DeepBlueR Farhad Shokoohi Package DMCHMM is not installed Leonardo Collado Torres Package DMCHMM is not installed Shepherd, Lori Package DMCHMM is not installed Michael Lawrence GenomicRanges::cbind() problem Aditya Bhagwat Creating an org.Hs.uniprot.db package Farhad Shokoohi Package DMCHMM is not installed Robert Castelo GenomicRanges::cbind() problem

Monday, September 11, 2017 37 emails

Sunday, September 10, 2017 2 emails

Nima Hejazi Bioconductor package landing pages Levi Waldron coerce ExpressionSet to SummarizedExperiment

Saturday, September 9, 2017 8 emails

Charles Warden COHCAP GitHub Update Martin Morgan COHCAP GitHub Update Sean Davis COHCAP GitHub Update Charles Warden COHCAP GitHub Update Henrik Bengtsson NEWS, inst/NEWS, NEWS.md Nan Xiao pandoc SSL error on malbec2 and tokay2 Martin Morgan NEWS, inst/NEWS, NEWS.md Levi Waldron NEWS, inst/NEWS, NEWS.md

Friday, September 8, 2017 25 emails

Thursday, September 7, 2017 8 emails

Thomas Girke Duplicate commit error on and off Turaga, Nitesh Duplicate commit error on and off Hervé Pagès experimental data packages and git-lfs Levi Waldron experimental data packages and git-lfs Turaga, Nitesh problem with git / svn transition: ssh keys Turaga, Nitesh experimental data packages and git-lfs Michael Lawrence role of replaceSlots in BiocGenerics Emily Packer eLife supports development of open technology stack for publishing reproducible manuscripts online

Wednesday, September 6, 2017 25 emails

Hervé Pagès role of replaceSlots in BiocGenerics Hervé Pagès role of replaceSlots in BiocGenerics Hervé Pagès role of replaceSlots in BiocGenerics Michael Lawrence role of replaceSlots in BiocGenerics Vincent Carey role of replaceSlots in BiocGenerics Hervé Pagès role of replaceSlots in BiocGenerics Michael Lawrence role of replaceSlots in BiocGenerics Jim Hester Bioconductor-mirror permanently removed August 25th Vincent Carey role of replaceSlots in BiocGenerics Levi Waldron experimental data packages and git-lfs Martin Morgan pandoc SSL error on malbec2 and tokay2 Blattmann Peter Problems pushing changes from github to git.bioconductor Blattmann Peter Problems pushing changes from github to git.bioconductor Hervé Pagès Bioconductor package landing pages Michael Lawrence splitting a Bioconductor package in two Stephanie M. Gogarten splitting a Bioconductor package in two Andrzej Oleś workflow building issues on mac and windows Shepherd, Lori Bioconductor-mirror permanently removed August 25th Martin Morgan Bioconductor-mirror permanently removed August 25th Robert M. Flight Bioconductor-mirror permanently removed August 25th Turaga, Nitesh Bioconductor-mirror permanently removed August 25th Jim Hester Bioconductor-mirror permanently removed August 25th Simina Boca updating Bioconductor package that is already on Github Shepherd, Lori updating Bioconductor package that is already on Github Sean Davis updating Bioconductor package that is already on Github

Tuesday, September 5, 2017 10 emails

Simina Boca updating Bioconductor package that is already on Github Turaga, Nitesh experimental data packages and git-lfs Levi Waldron experimental data packages and git-lfs Levi Waldron experimental data packages and git-lfs Nima Hejazi Bioconductor package landing pages Shepherd, Lori Resubmit package Hu, Zicheng Resubmit package Leonardo Collado Torres workflow building issues on mac and windows Nan Xiao pandoc SSL error on malbec2 and tokay2 Kasper Daniel Hansen pandoc SSL error on malbec2 and tokay2

Monday, September 4, 2017 7 emails

Sean Davis COHCAP GitHub Update Charles Warden COHCAP GitHub Update Sean Davis COHCAP GitHub Update Charles Warden COHCAP GitHub Update Nan Xiao pandoc SSL error on malbec2 and tokay2 Turaga, Nitesh git transition: unrelated histories Fabian Müller git transition: unrelated histories

Sunday, September 3, 2017 5 emails

Turaga, Nitesh COHCAP GitHub Update Matt Ritchie BioCAsia, 17th November 2017, Adelaide, Australia Charles Warden COHCAP GitHub Update Pariksheet Nanda Cannot install Bioconductor packages with biocLite() after loading QuasR Laurent Gatto Identical methods in two packages

Friday, September 1, 2017 13 emails

Dario Strbenac how to verify upstream git changes Robert Castelo how to verify upstream git changes Turaga, Nitesh Bioconductor-mirror permanently removed August 25th Turaga, Nitesh git transition: unrelated histories Laurent Gatto Ontology generic Hervé Pagès Ontology generic Turaga, Nitesh how to verify upstream git changes Robert Castelo how to verify upstream git changes Andrzej Oleś workflow building issues on mac and windows Turaga, Nitesh Problems pushing changes from github to git.bioconductor Laurent Gatto Ontology generic Blattmann Peter Problems pushing changes from github to git.bioconductor Fabian Müller git transition: unrelated histories

Bioc-devel September 2017